[BioC] a question about trimLRPatterns?

[wang peter]

hello all:

i want to know how this function process data?

for left match
it is taken as a "rate" and is converted to
max.Lmismatch=as.integer(1:nLp *rate )
then it try to match between the suffix substring(Lpattern, nLp - i + 1, nLp)
of Lpattern and the first i letters of subject.
dees i start from 1 or nLp? and the corresponding allowed mismatch is
max.Lmismatch[i]?

for the right match
it is taken as a "rate" and is converted to
max.Rmismatch=as.integer(1:nRp * rate)
then it try to match between the suffix substring(Rpattern, nRp - i + 1, nRp)
of subject and the first i letters of Rpattern.
dees i start from 1 or nRp? and the corresponding allowed mismatch is
max.Rmismatch[i]?

-- 
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute
Cornell University
Tower Road, Ithaca, NY 14853-1801
Office phone: 1-607-254-1267(day)
Official email:sg839 at cornell.edu
Facebook:http://www.facebook.com/profile.php?id=100001986532253